OK. Making a lot more sense. You transplanted a 1997 engine with a 1997 Engine harness into a 1998 Chassis.. Then trying to use the 1998 Body harness and ECU to run this rig.
I have never done engine swaps that way. I always stuck with the Chassis wiring and all harnesses with the power train parts in Toyotas. Even when I swapped an engine on a 1991 Camry into a 1990 Camry. I kept the 1990 wiring on the engine.
Almost always a few changes between model years and sometimes even accessories.
I miss the old years in the 80's the rigs only had one harness for all models so you could add the accessories that were missing the base models etc as they all used the same harness and the plugs were all there.. :-)
For Sleepy Dad focus on the Engine harness and the ECU see what is different as you are probably use one or 2 wires missing or different.
As for the next swap it maybe best to swap the engine harness to match the chassis so your not pulling your hair out like you are now.
I was thinking you swapped the transmission as well as they maybe differences on that was well but that is part of the engine harness.
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7 3rd gens listed in the build thread (2 are parts mobiles)
Build Thread:
https://www.toyota-4runner.org/3rd-g...os-builds.html
Brillo's Bucket Fluid Ex changer:
https://www.toyota-4runner.org/3rd-g...ml#post3358086
Sparks Plugs Wire and Coil Information:
https://www.toyota-4runner.org/3rd-g...on-5vz-fe.html